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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgccgacaatttcagccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgttt...

Basic information

species Zea mays
transcript GRMZM2G025470_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G025470_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g51500.3 (Oryza sativa), 5'ss of exon 2
AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgccgacaatttca--gccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgttt
|||||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||     | |||| |||| ||  ||||  ||||| |  |||      | ||   |||| | |  | | |   || |  | |   |
AACCGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAgtggtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacaca--aaactctattaaat

upper sequence: GRMZM2G025470_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g51500.2 (Oryza sativa), 5'ss of exon 2
AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgccgacaatttcag--ccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgttt-
   ||||||||||| |||||||||||||||||||||||| | ||||| |||||||||||||||||||||||||| || ||||||||| | |||||||||||||||||||||| ||||||     | |||| |||| ||  ||||  ||||| |  |||      | ||   |||| | |  | | |      |      ||  
---CGGACACTTGCTGAGTCCCGTGTTCCAGTAGGAGAGGTTCCAGGAGGTGTAATTACAATGCATGTGGTAGTACGCCCTCCACAACCCGACAAAAACAGTGgtattgccgccaattttgtttcttttttttcacattgtttttctggctgcactgatggcctatttcgcttctccgttgacacaaaactctattaaattca
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|32845497|gb|CD985178.1|CD985178
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32845497|gb|CD985178.1|CD985178
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32845497|gb|CD985178.1|CD985178
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32845497|gb|CD985178.1|CD985178
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32914897|gb|CF019709.1|CF019709
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32914897|gb|CF019709.1|CF019709
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32914897|gb|CF019709.1|CF019709
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32914897|gb|CF019709.1|CF019709
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32921127|gb|CF025939.1|CF025939
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
EST: gi|32851050|gb|CD990731.1|CD990731
EST:     TGTAATTACAATGCATGTGGTAGGGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32851050|gb|CD990731.1|CD990731
EST:     TGTAATTACAATGCATGTGGTAGGGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32851050|gb|CD990731.1|CD990731
EST:     TGTAATTACAATGCATGTGGTAGGGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32851050|gb|CD990731.1|CD990731
EST:     TGTAATTACAATGCATGTGGTAGGGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211407976|gb|FL261730.1|FL261730
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
EST: gi|13126515|gb|BG317085.1|BG317085
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|13126515|gb|BG317085.1|BG317085
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|13126515|gb|BG317085.1|BG317085
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|13126515|gb|BG317085.1|BG317085
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|14203831|gb|BG837508.1|BG837508
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
EST: gi|211407973|gb|FL261727.1|FL261727
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
EST: gi|32851133|gb|CD990814.1|CD990814
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32851133|gb|CD990814.1|CD990814
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32851133|gb|CD990814.1|CD990814
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|32851133|gb|CD990814.1|CD990814
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410514|gb|FL261735.1|FL261735
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410514|gb|FL261735.1|FL261735
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410514|gb|FL261735.1|FL261735
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410514|gb|FL261735.1|FL261735
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410522|gb|FL261743.1|FL261743
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410522|gb|FL261743.1|FL261743
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410522|gb|FL261743.1|FL261743
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211410522|gb|FL261743.1|FL261743
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|211340532|gb|FL467124.1|FL467124
EST:     TGTAATTACAATGCATGTGGTAGTGCGACCTCCACAAGCTGACAAAAACA                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
EST: gi|78117275|gb|DV535662.1|DV535662
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         AGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTC
EST: gi|16377623|gb|BI992025.1|BI992025
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|16377623|gb|BI992025.1|BI992025
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|16377623|gb|BI992025.1|BI992025
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|16377623|gb|BI992025.1|BI992025
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|109179560|gb|EC380070.1|EC380070
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|109179560|gb|EC380070.1|EC380070
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|109179560|gb|EC380070.1|EC380070
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-
EST: gi|109179560|gb|EC380070.1|EC380070
EST:     TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACA                         G
genomic: TGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccag-

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 34 (upstream exon), 48 (downstream exon)
Score: 15

AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTCTCTGATAAGGCGTCTGCTTGGTGCTGTACAATCTGTGTGTACACATAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 107

AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTCTCTGATAAGGCGTCTGCTTGGTGCTGTACAATCTGTGTGTACACATAAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 198

AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTCTCTGATAAGGCGTCTGCTTGGTGCTGTACAATCTGTGTGTACACATAAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 52

AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgc ... actttcccagAGAAGCAGCTTGCCAATTCCCCCAAGCAGAACAGATGTGGATGCACCATTCTCTGATAAGGCGTCTGCTTGGTGCTGTACAATCTGTGTGTACACATAAG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACCGGACACTTGCAGAGTCCCGTGTTCCAGTAGGAGAGATCCCAGGTGGTGTAATTACAATGCATGTGGTAGTGCGGCCTCCACAAGCTGACAAAAACAgtggtattgccgacaatttcagccttttattcatatcattttcttggctcccatgagaaataacttgaattctacttccatatattgaattgaagtgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaataa